Fig. S1 Structural and CpG methylation changes during allopolyploid speciation in Spartina.

Fig. S2 Methylation levels of methyl-sensitive transposon display (MSTD) bands for each of thethree TEs and methyl-sensitive amplified polymorphism (MSAP) bands in theparental species, Spartina alterniflora and Spartina maritima,the independent homoploid F1 hybrids Spartina × neyrautii and Spartina × townsendii,and the natural allopolyploid Spartina anglica.

Notes S1 Detailedprotocol of methyl-sensitive transposon display (MSTD).

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